Rebase into tool request...

jmchilton · Sep 1, 2024 · befd96c · befd96c
1 parent 5bbf756
commit befd96c
Show file tree

Hide file tree

Showing 4 changed files with 17 additions and 8 deletions.
diff --git a/.github/workflows/framework_tools.yaml b/.github/workflows/framework_tools.yaml
@@ -26,7 +26,7 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.8']
-        use-legacy-api: ['if_needed', 'never']
+        use-legacy-api: ['if_needed', 'always']
     services:
       postgres:
         image: postgres:13

diff --git a/lib/galaxy/tool_util/parameters/visitor.py b/lib/galaxy/tool_util/parameters/visitor.py
@@ -18,8 +18,17 @@
 )
 from .state import ToolState
 
-VISITOR_NO_REPLACEMENT = object()
-VISITOR_UNDEFINED = object()
+
+class VisitorNoReplacement:
+    pass
+
+
+class VisitorUndefined:
+    pass
+
+
+VISITOR_NO_REPLACEMENT = VisitorNoReplacement()
+VISITOR_UNDEFINED = VisitorUndefined()
 
 
 class Callback(Protocol):
@@ -51,11 +60,11 @@ def _visit_input_values(
     for model in input_models:
         name = model.name
         input_value = input_values.get(name, VISITOR_UNDEFINED)
+        if input_value is VISITOR_UNDEFINED:
+            continue
         replacement = callback(model, input_value)
         if replacement != no_replacement_value:
             new_input_values[name] = replacement
-        elif replacement is VISITOR_UNDEFINED:
-            pass
         else:
             new_input_values[name] = input_value
     return new_input_values

diff --git a/lib/galaxy/tool_util/verify/interactor.py b/lib/galaxy/tool_util/verify/interactor.py
@@ -670,7 +670,7 @@ def run_tool(
             parameters = request_schema["parameters"]
 
             def adapt_datasets(test_input: JsonTestDatasetDefDict) -> DataRequest:
-                return DataRequest(**self.uploads(test_input["path"]))
+                return DataRequest(**self.uploads[test_input["path"]])
 
             def adapt_collections(test_input: JsonTestCollectionDefDict) -> DataCollectionRequest:
                 test_collection_def = TestCollectionDef.from_dict(test_input)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
@@ -1844,7 +1844,7 @@ def expand_incoming_async(self, request_context: WorkRequestContext, tool_reques
 
         job_tool_states: List[JobInternalToolState]
         collection_info: Optional[MatchingCollections]
-        job_tool_states, collection_info = expand_meta_parameters_async(trans.app, self, tool_request_internal_state)
+        job_tool_states, collection_info = expand_meta_parameters_async(request_context.app, self, tool_request_internal_state)
 
         self._ensure_expansion_is_valid(job_tool_states, rerun_remap_job_id)
 
@@ -1856,7 +1856,7 @@ def expand_incoming_async(self, request_context: WorkRequestContext, tool_reques
         all_errors = []
         all_params: List[ToolStateJobInstancePopulatedT] = []
         for expanded_incoming in job_tool_states:
-            params, errors = self._populate(request_context, expanded_incoming, input_format)
+            params, errors = self._populate(request_context, expanded_incoming, "21.01")
             all_errors.append(errors)
             all_params.append(params)
         unset_dataset_matcher_factory(request_context)